Starting phenix.real_space_refine on Wed Mar 12 21:38:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvm_32144/03_2025/7vvm_32144.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvm_32144/03_2025/7vvm_32144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vvm_32144/03_2025/7vvm_32144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvm_32144/03_2025/7vvm_32144.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvm_32144/03_2025/7vvm_32144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvm_32144/03_2025/7vvm_32144.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5405 2.51 5 N 1486 2.21 5 O 1564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1893 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2508 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 389 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 217 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2536 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 409 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 362 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 5, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 284 Time building chain proxies: 4.82, per 1000 atoms: 0.57 Number of scatterers: 8507 At special positions: 0 Unit cell: (127.267, 105.134, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1564 8.00 N 1486 7.00 C 5405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.07 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 972.2 milliseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 41.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.269A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.503A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.503A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.518A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.945A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.562A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.677A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.575A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.687A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL R 193 " --> pdb=" O MET R 189 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 removed outlier: 3.570A pdb=" N PHE R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.923A pdb=" N VAL R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 347 removed outlier: 3.763A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.619A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 391 removed outlier: 3.570A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.617A pdb=" N LEU R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 418 removed outlier: 3.700A pdb=" N TYR R 403 " --> pdb=" O THR R 399 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET R 414 " --> pdb=" O THR R 410 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.633A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 477 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.611A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.611A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.511A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.691A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.750A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.823A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.711A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.501A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.426A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.604A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.576A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 449 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1409 1.31 - 1.44: 2401 1.44 - 1.58: 4798 1.58 - 1.72: 0 1.72 - 1.85: 76 Bond restraints: 8684 Sorted by residual: bond pdb=" N VAL R 157 " pdb=" CA VAL R 157 " ideal model delta sigma weight residual 1.460 1.503 -0.043 7.50e-03 1.78e+04 3.30e+01 bond pdb=" C ALA B 287 " pdb=" O ALA B 287 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.21e-02 6.83e+03 2.97e+01 bond pdb=" C VAL B 100 " pdb=" O VAL B 100 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.04e-02 9.25e+03 2.96e+01 bond pdb=" C TYR B 124 " pdb=" O TYR B 124 " ideal model delta sigma weight residual 1.236 1.301 -0.065 1.21e-02 6.83e+03 2.88e+01 bond pdb=" CE1 HIS A 377 " pdb=" NE2 HIS A 377 " ideal model delta sigma weight residual 1.321 1.371 -0.050 1.00e-02 1.00e+04 2.46e+01 ... (remaining 8679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 9024 2.13 - 4.26: 2633 4.26 - 6.39: 142 6.39 - 8.52: 6 8.52 - 10.65: 2 Bond angle restraints: 11807 Sorted by residual: angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 113.57 120.74 -7.17 1.31e+00 5.83e-01 2.99e+01 angle pdb=" N GLN R 451 " pdb=" CA GLN R 451 " pdb=" C GLN R 451 " ideal model delta sigma weight residual 110.97 105.73 5.24 1.09e+00 8.42e-01 2.32e+01 angle pdb=" CA VAL R 439 " pdb=" C VAL R 439 " pdb=" O VAL R 439 " ideal model delta sigma weight residual 121.05 115.76 5.29 1.11e+00 8.12e-01 2.27e+01 angle pdb=" N ILE A 372 " pdb=" CA ILE A 372 " pdb=" C ILE A 372 " ideal model delta sigma weight residual 110.72 106.02 4.70 1.01e+00 9.80e-01 2.16e+01 angle pdb=" C LYS R 34 " pdb=" N GLU R 35 " pdb=" CA GLU R 35 " ideal model delta sigma weight residual 120.54 126.82 -6.28 1.35e+00 5.49e-01 2.16e+01 ... (remaining 11802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 4632 16.64 - 33.28: 396 33.28 - 49.92: 56 49.92 - 66.56: 13 66.56 - 83.20: 14 Dihedral angle restraints: 5111 sinusoidal: 1822 harmonic: 3289 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 172.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 649 0.058 - 0.117: 466 0.117 - 0.175: 186 0.175 - 0.233: 44 0.233 - 0.291: 7 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA PRO A 351 " pdb=" N PRO A 351 " pdb=" C PRO A 351 " pdb=" CB PRO A 351 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1349 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " 0.013 2.00e-02 2.50e+03 1.04e-02 2.68e+00 pdb=" CG TRP A 234 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 378 " -0.020 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE R 378 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE R 378 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 378 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 378 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 378 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 378 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 352 " 0.015 2.00e-02 2.50e+03 1.20e-02 2.14e+00 pdb=" CG HIS A 352 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS A 352 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 352 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 352 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 352 " 0.007 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 8636 3.28 - 3.82: 13249 3.82 - 4.36: 17850 4.36 - 4.90: 29450 Nonbonded interactions: 69701 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.200 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.300 3.040 nonbonded pdb=" O SER R 356 " pdb=" OG SER R 356 " model vdw 2.304 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.322 3.040 ... (remaining 69696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.101 8684 Z= 0.995 Angle : 1.761 10.650 11807 Z= 1.280 Chirality : 0.086 0.291 1352 Planarity : 0.003 0.012 1514 Dihedral : 13.507 83.200 2972 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.60 % Allowed : 4.06 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1113 helix: -0.46 (0.23), residues: 430 sheet: -0.85 (0.33), residues: 226 loop : -0.84 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP B 297 HIS 0.005 0.001 HIS A 352 PHE 0.020 0.003 PHE R 378 TYR 0.015 0.003 TYR N 60 ARG 0.006 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.969 Fit side-chains REVERT: A 16 GLU cc_start: 0.6489 (tp30) cc_final: 0.5699 (tm-30) REVERT: A 216 LYS cc_start: 0.7371 (mptt) cc_final: 0.7127 (mmtt) REVERT: A 221 MET cc_start: 0.7791 (ttt) cc_final: 0.7457 (ttp) REVERT: A 258 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7217 (mp0) REVERT: A 325 THR cc_start: 0.8530 (m) cc_final: 0.8325 (m) REVERT: A 379 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.6980 (ttm110) REVERT: A 382 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6999 (mm-30) REVERT: B 80 ILE cc_start: 0.8221 (mt) cc_final: 0.8021 (mm) REVERT: B 137 ARG cc_start: 0.6551 (ttm110) cc_final: 0.5769 (ttm-80) REVERT: B 181 THR cc_start: 0.7741 (m) cc_final: 0.7530 (p) REVERT: B 197 ARG cc_start: 0.6105 (mmp-170) cc_final: 0.5892 (mmm160) REVERT: B 220 GLN cc_start: 0.7424 (mt0) cc_final: 0.6993 (mt0) REVERT: B 264 TYR cc_start: 0.7883 (m-80) cc_final: 0.7269 (m-80) REVERT: B 277 SER cc_start: 0.8783 (t) cc_final: 0.8316 (m) REVERT: B 289 TYR cc_start: 0.9113 (m-80) cc_final: 0.8723 (m-80) REVERT: B 322 ASP cc_start: 0.7872 (m-30) cc_final: 0.7023 (t0) REVERT: G 42 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6939 (mt-10) REVERT: G 44 HIS cc_start: 0.6819 (m90) cc_final: 0.6608 (m170) REVERT: G 62 ARG cc_start: 0.4738 (pmt-80) cc_final: 0.3603 (mmm160) REVERT: N 3 GLN cc_start: 0.6269 (tt0) cc_final: 0.5545 (tp-100) REVERT: N 19 ARG cc_start: 0.7322 (ttt90) cc_final: 0.7062 (ttt-90) REVERT: N 82 GLN cc_start: 0.6016 (tp40) cc_final: 0.5136 (tp-100) REVERT: N 83 MET cc_start: 0.6351 (mtt) cc_final: 0.5925 (mpp) REVERT: N 93 VAL cc_start: 0.7778 (t) cc_final: 0.7540 (p) REVERT: N 94 TYR cc_start: 0.8466 (m-80) cc_final: 0.7815 (m-80) REVERT: R 282 ARG cc_start: 0.7013 (mpt-90) cc_final: 0.6724 (mmt90) REVERT: R 291 PHE cc_start: 0.8031 (m-10) cc_final: 0.7733 (m-10) REVERT: R 360 LYS cc_start: 0.4708 (ptmt) cc_final: 0.4498 (ptmt) REVERT: R 363 ILE cc_start: 0.7763 (mm) cc_final: 0.7487 (tt) REVERT: R 372 VAL cc_start: 0.7205 (m) cc_final: 0.6989 (t) REVERT: R 383 ARG cc_start: 0.6956 (tmm-80) cc_final: 0.6714 (tmm-80) REVERT: R 391 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7566 (mt-10) REVERT: R 399 THR cc_start: 0.5947 (t) cc_final: 0.5636 (p) REVERT: R 439 VAL cc_start: 0.4753 (p) cc_final: 0.4292 (m) REVERT: R 443 TYR cc_start: 0.7097 (t80) cc_final: 0.6775 (t80) REVERT: R 445 MET cc_start: 0.7668 (mmm) cc_final: 0.7223 (mmp) REVERT: R 462 CYS cc_start: 0.6426 (m) cc_final: 0.6098 (t) REVERT: R 473 SER cc_start: 0.4742 (m) cc_final: 0.4528 (t) outliers start: 5 outliers final: 2 residues processed: 206 average time/residue: 0.2755 time to fit residues: 73.0493 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 254 ASN A 284 GLN B 239 ASN B 340 ASN N 39 GLN P 14 HIS R 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.161936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127617 restraints weight = 11095.805| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.28 r_work: 0.3422 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8684 Z= 0.172 Angle : 0.543 6.020 11807 Z= 0.298 Chirality : 0.041 0.149 1352 Planarity : 0.004 0.027 1514 Dihedral : 4.490 33.310 1217 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.15 % Allowed : 9.55 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1113 helix: 1.04 (0.25), residues: 433 sheet: -0.53 (0.34), residues: 219 loop : -0.45 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS P 9 PHE 0.015 0.001 PHE R 335 TYR 0.019 0.001 TYR R 191 ARG 0.004 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6876 (tppt) cc_final: 0.6213 (tmtt) REVERT: A 216 LYS cc_start: 0.7105 (mptt) cc_final: 0.6697 (mmtt) REVERT: A 221 MET cc_start: 0.7777 (ttt) cc_final: 0.7493 (ttp) REVERT: A 258 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7464 (mp0) REVERT: A 379 ARG cc_start: 0.6874 (mtm-85) cc_final: 0.6524 (ttp-110) REVERT: B 20 ASP cc_start: 0.6973 (m-30) cc_final: 0.6641 (m-30) REVERT: B 68 ARG cc_start: 0.7401 (ttt180) cc_final: 0.7105 (ttt90) REVERT: B 82 TRP cc_start: 0.8534 (m100) cc_final: 0.8149 (m100) REVERT: B 137 ARG cc_start: 0.6439 (ttm110) cc_final: 0.5851 (ttm-80) REVERT: B 197 ARG cc_start: 0.6194 (mmp-170) cc_final: 0.5958 (mmm160) REVERT: B 220 GLN cc_start: 0.7336 (mt0) cc_final: 0.7078 (tt0) REVERT: B 262 MET cc_start: 0.7115 (tpp) cc_final: 0.6867 (tpt) REVERT: B 264 TYR cc_start: 0.7542 (m-80) cc_final: 0.7122 (m-80) REVERT: B 277 SER cc_start: 0.8683 (t) cc_final: 0.8233 (m) REVERT: B 322 ASP cc_start: 0.7439 (m-30) cc_final: 0.6688 (t0) REVERT: G 42 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6960 (mt-10) REVERT: G 44 HIS cc_start: 0.6949 (m90) cc_final: 0.6532 (m170) REVERT: G 62 ARG cc_start: 0.4716 (pmt-80) cc_final: 0.3552 (mmm-85) REVERT: N 77 ASN cc_start: 0.6694 (m-40) cc_final: 0.6297 (t0) REVERT: N 93 VAL cc_start: 0.7717 (t) cc_final: 0.7357 (p) REVERT: N 94 TYR cc_start: 0.8185 (m-80) cc_final: 0.7627 (m-80) REVERT: R 186 ARG cc_start: 0.4183 (mtt180) cc_final: 0.3833 (mtt180) REVERT: R 315 PHE cc_start: 0.5621 (t80) cc_final: 0.5412 (t80) REVERT: R 331 LEU cc_start: 0.7265 (tt) cc_final: 0.7058 (tp) REVERT: R 360 LYS cc_start: 0.5025 (ptmt) cc_final: 0.4783 (ptmt) REVERT: R 391 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6794 (mt-10) REVERT: R 399 THR cc_start: 0.5973 (t) cc_final: 0.5617 (m) REVERT: R 439 VAL cc_start: 0.4876 (p) cc_final: 0.4377 (m) REVERT: R 441 MET cc_start: 0.5757 (mmt) cc_final: 0.5230 (mmt) REVERT: R 445 MET cc_start: 0.7155 (mmm) cc_final: 0.6920 (mmt) REVERT: R 465 GLU cc_start: 0.6102 (tp30) cc_final: 0.5889 (tp30) outliers start: 18 outliers final: 11 residues processed: 179 average time/residue: 0.2468 time to fit residues: 58.4592 Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 75 GLN B 155 ASN P 9 HIS R 295 ASN R 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.165218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132614 restraints weight = 11110.133| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.11 r_work: 0.3412 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8684 Z= 0.263 Angle : 0.549 5.646 11807 Z= 0.299 Chirality : 0.042 0.152 1352 Planarity : 0.004 0.034 1514 Dihedral : 4.279 18.050 1215 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.63 % Allowed : 12.05 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1113 helix: 1.13 (0.25), residues: 434 sheet: -0.33 (0.34), residues: 214 loop : -0.45 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.012 0.002 HIS P 14 PHE 0.016 0.002 PHE R 335 TYR 0.019 0.002 TYR R 191 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7089 (tppt) cc_final: 0.6441 (tmtt) REVERT: A 59 GLN cc_start: 0.6481 (mt0) cc_final: 0.6097 (mm-40) REVERT: A 216 LYS cc_start: 0.7181 (mptt) cc_final: 0.6707 (mmtt) REVERT: A 240 ASP cc_start: 0.7245 (p0) cc_final: 0.7024 (p0) REVERT: A 258 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7322 (mp0) REVERT: B 20 ASP cc_start: 0.6654 (m-30) cc_final: 0.6283 (m-30) REVERT: B 68 ARG cc_start: 0.7457 (ttt180) cc_final: 0.7142 (ttt90) REVERT: B 137 ARG cc_start: 0.6663 (ttm110) cc_final: 0.5980 (ttm-80) REVERT: B 220 GLN cc_start: 0.7228 (mt0) cc_final: 0.6977 (mt0) REVERT: B 277 SER cc_start: 0.8665 (t) cc_final: 0.8229 (m) REVERT: B 322 ASP cc_start: 0.7529 (m-30) cc_final: 0.6716 (t0) REVERT: G 42 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6938 (mt-10) REVERT: G 44 HIS cc_start: 0.6909 (m90) cc_final: 0.6510 (m-70) REVERT: G 62 ARG cc_start: 0.4749 (pmt-80) cc_final: 0.3693 (mmm160) REVERT: N 4 LEU cc_start: 0.7296 (mt) cc_final: 0.7027 (mt) REVERT: N 77 ASN cc_start: 0.6592 (m-40) cc_final: 0.6259 (t0) REVERT: N 94 TYR cc_start: 0.8228 (m-80) cc_final: 0.7685 (m-80) REVERT: R 360 LYS cc_start: 0.5423 (ptmt) cc_final: 0.5196 (ptmt) REVERT: R 391 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6374 (mt-10) REVERT: R 399 THR cc_start: 0.5852 (t) cc_final: 0.5457 (m) REVERT: R 405 LYS cc_start: 0.6527 (ttmm) cc_final: 0.6259 (tppt) REVERT: R 407 LEU cc_start: 0.7239 (tp) cc_final: 0.7019 (mt) REVERT: R 441 MET cc_start: 0.5908 (mmt) cc_final: 0.5365 (mmt) REVERT: R 465 GLU cc_start: 0.5789 (tp30) cc_final: 0.5574 (tp30) outliers start: 22 outliers final: 17 residues processed: 161 average time/residue: 0.2608 time to fit residues: 55.4943 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 25 optimal weight: 0.0370 chunk 75 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 254 ASN N 3 GLN P 9 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.169128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136861 restraints weight = 10976.283| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.11 r_work: 0.3534 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8684 Z= 0.125 Angle : 0.451 5.605 11807 Z= 0.248 Chirality : 0.039 0.157 1352 Planarity : 0.003 0.034 1514 Dihedral : 3.835 16.054 1215 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.15 % Allowed : 14.08 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1113 helix: 1.63 (0.26), residues: 428 sheet: -0.10 (0.35), residues: 206 loop : -0.30 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS P 14 PHE 0.020 0.001 PHE R 335 TYR 0.017 0.001 TYR R 191 ARG 0.003 0.000 ARG R 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6003 (mt0) cc_final: 0.5790 (mm-40) REVERT: A 216 LYS cc_start: 0.7187 (mptt) cc_final: 0.6697 (mmtt) REVERT: A 258 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7355 (mp0) REVERT: B 20 ASP cc_start: 0.6374 (m-30) cc_final: 0.6053 (m-30) REVERT: B 68 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7067 (ttt90) REVERT: B 197 ARG cc_start: 0.6392 (mmp-170) cc_final: 0.5723 (mmm160) REVERT: B 217 MET cc_start: 0.7425 (mtt) cc_final: 0.7050 (mtm) REVERT: B 220 GLN cc_start: 0.7321 (mt0) cc_final: 0.6961 (mt0) REVERT: B 277 SER cc_start: 0.8619 (t) cc_final: 0.8254 (m) REVERT: B 322 ASP cc_start: 0.7340 (m-30) cc_final: 0.6512 (t0) REVERT: G 42 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7187 (mt-10) REVERT: G 62 ARG cc_start: 0.4908 (pmt-80) cc_final: 0.3897 (mmm160) REVERT: N 46 GLU cc_start: 0.7604 (pt0) cc_final: 0.7265 (mt-10) REVERT: N 77 ASN cc_start: 0.6518 (m-40) cc_final: 0.6315 (t0) REVERT: N 94 TYR cc_start: 0.8111 (m-80) cc_final: 0.7669 (m-80) REVERT: N 106 ASP cc_start: 0.7112 (p0) cc_final: 0.6785 (p0) REVERT: R 240 LYS cc_start: 0.5454 (OUTLIER) cc_final: 0.4561 (tptp) REVERT: R 292 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6764 (tp) REVERT: R 405 LYS cc_start: 0.6443 (ttmm) cc_final: 0.6173 (tppt) REVERT: R 439 VAL cc_start: 0.5011 (p) cc_final: 0.4449 (m) REVERT: R 441 MET cc_start: 0.5880 (mmt) cc_final: 0.5670 (mmt) REVERT: R 465 GLU cc_start: 0.5844 (tp30) cc_final: 0.5548 (tp30) outliers start: 18 outliers final: 9 residues processed: 173 average time/residue: 0.3053 time to fit residues: 70.2690 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 240 LYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 56 optimal weight: 0.0570 chunk 79 optimal weight: 0.3980 chunk 67 optimal weight: 8.9990 chunk 76 optimal weight: 40.0000 chunk 33 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 HIS R 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134418 restraints weight = 10930.315| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.17 r_work: 0.3434 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8684 Z= 0.215 Angle : 0.493 5.570 11807 Z= 0.270 Chirality : 0.041 0.162 1352 Planarity : 0.004 0.040 1514 Dihedral : 3.974 15.755 1215 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.98 % Allowed : 15.63 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1113 helix: 1.44 (0.25), residues: 434 sheet: -0.10 (0.33), residues: 214 loop : -0.39 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS P 14 PHE 0.023 0.002 PHE R 315 TYR 0.021 0.002 TYR R 191 ARG 0.005 0.001 ARG R 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.5892 (mt0) cc_final: 0.5671 (mm-40) REVERT: A 216 LYS cc_start: 0.7177 (mptt) cc_final: 0.6686 (mmtt) REVERT: A 258 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7436 (mp0) REVERT: A 346 ARG cc_start: 0.6197 (mtt180) cc_final: 0.5856 (mmt-90) REVERT: B 20 ASP cc_start: 0.6262 (m-30) cc_final: 0.5947 (m-30) REVERT: B 68 ARG cc_start: 0.7423 (ttt180) cc_final: 0.7008 (ttt90) REVERT: B 220 GLN cc_start: 0.7460 (mt0) cc_final: 0.7048 (tt0) REVERT: B 264 TYR cc_start: 0.7340 (m-80) cc_final: 0.6838 (m-80) REVERT: B 277 SER cc_start: 0.8628 (t) cc_final: 0.8208 (m) REVERT: B 322 ASP cc_start: 0.7486 (m-30) cc_final: 0.6718 (t0) REVERT: G 42 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7029 (mt-10) REVERT: G 62 ARG cc_start: 0.4905 (pmt-80) cc_final: 0.3776 (mmm-85) REVERT: N 46 GLU cc_start: 0.7532 (pt0) cc_final: 0.7240 (mt-10) REVERT: N 77 ASN cc_start: 0.6445 (m-40) cc_final: 0.6158 (t0) REVERT: N 94 TYR cc_start: 0.8244 (m-80) cc_final: 0.7757 (m-80) REVERT: N 106 ASP cc_start: 0.7145 (p0) cc_final: 0.6762 (p0) REVERT: R 233 ARG cc_start: 0.7378 (ttt180) cc_final: 0.7100 (ttt180) REVERT: R 240 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.4553 (tptp) REVERT: R 292 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6648 (tp) REVERT: R 391 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6828 (mt-10) REVERT: R 441 MET cc_start: 0.5980 (mmt) cc_final: 0.5548 (mmt) REVERT: R 465 GLU cc_start: 0.5892 (tp30) cc_final: 0.5624 (tp30) outliers start: 25 outliers final: 20 residues processed: 150 average time/residue: 0.3025 time to fit residues: 60.7724 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 8 MET Chi-restraints excluded: chain R residue 240 LYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.169884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137855 restraints weight = 10706.598| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.10 r_work: 0.3474 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8684 Z= 0.143 Angle : 0.446 5.555 11807 Z= 0.246 Chirality : 0.040 0.159 1352 Planarity : 0.003 0.038 1514 Dihedral : 3.798 14.890 1215 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.51 % Allowed : 17.06 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1113 helix: 1.82 (0.26), residues: 425 sheet: 0.01 (0.34), residues: 212 loop : -0.33 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS P 14 PHE 0.026 0.001 PHE R 315 TYR 0.019 0.001 TYR R 191 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7166 (mptt) cc_final: 0.6665 (mmtt) REVERT: A 258 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7362 (mp0) REVERT: A 379 ARG cc_start: 0.6911 (ttm110) cc_final: 0.6699 (ttm110) REVERT: B 20 ASP cc_start: 0.6223 (m-30) cc_final: 0.5937 (m-30) REVERT: B 68 ARG cc_start: 0.7401 (ttt180) cc_final: 0.6997 (ttt90) REVERT: B 220 GLN cc_start: 0.7387 (mt0) cc_final: 0.7118 (tt0) REVERT: B 264 TYR cc_start: 0.7289 (m-80) cc_final: 0.6870 (m-80) REVERT: B 322 ASP cc_start: 0.7365 (m-30) cc_final: 0.6588 (t0) REVERT: G 42 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7066 (mt-10) REVERT: G 62 ARG cc_start: 0.4870 (pmt-80) cc_final: 0.3727 (mmm-85) REVERT: N 46 GLU cc_start: 0.7613 (pt0) cc_final: 0.7186 (mt-10) REVERT: N 77 ASN cc_start: 0.6395 (m-40) cc_final: 0.6152 (t0) REVERT: N 94 TYR cc_start: 0.8216 (m-80) cc_final: 0.7781 (m-80) REVERT: R 231 MET cc_start: 0.7390 (mtp) cc_final: 0.6991 (mtp) REVERT: R 233 ARG cc_start: 0.7227 (ttt180) cc_final: 0.6952 (ttt180) REVERT: R 240 LYS cc_start: 0.5498 (OUTLIER) cc_final: 0.4644 (tptp) REVERT: R 292 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6527 (tp) REVERT: R 391 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6756 (mt-10) REVERT: R 441 MET cc_start: 0.5948 (mmt) cc_final: 0.5673 (mmt) REVERT: R 465 GLU cc_start: 0.5879 (tp30) cc_final: 0.5603 (tp30) outliers start: 21 outliers final: 15 residues processed: 146 average time/residue: 0.2655 time to fit residues: 51.5047 Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 240 LYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135650 restraints weight = 10934.125| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.20 r_work: 0.3447 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8684 Z= 0.204 Angle : 0.472 5.575 11807 Z= 0.259 Chirality : 0.041 0.165 1352 Planarity : 0.003 0.040 1514 Dihedral : 3.926 15.122 1215 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.98 % Allowed : 17.18 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1113 helix: 1.59 (0.25), residues: 439 sheet: -0.04 (0.33), residues: 221 loop : -0.37 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.026 0.002 PHE R 315 TYR 0.020 0.001 TYR R 191 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7024 (mptt) cc_final: 0.6619 (mmtt) REVERT: A 258 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7369 (mp0) REVERT: B 20 ASP cc_start: 0.6295 (m-30) cc_final: 0.5974 (m-30) REVERT: B 68 ARG cc_start: 0.7421 (ttt180) cc_final: 0.6997 (ttt90) REVERT: B 220 GLN cc_start: 0.7322 (mt0) cc_final: 0.6998 (tt0) REVERT: B 264 TYR cc_start: 0.7398 (m-80) cc_final: 0.6930 (m-80) REVERT: B 322 ASP cc_start: 0.7460 (m-30) cc_final: 0.6716 (t0) REVERT: G 42 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7023 (mt-10) REVERT: G 62 ARG cc_start: 0.4720 (pmt-80) cc_final: 0.3732 (mmm-85) REVERT: N 46 GLU cc_start: 0.7578 (pt0) cc_final: 0.7257 (mt-10) REVERT: N 77 ASN cc_start: 0.6414 (m-40) cc_final: 0.6188 (t0) REVERT: N 94 TYR cc_start: 0.8233 (m-80) cc_final: 0.7589 (m-80) REVERT: N 124 VAL cc_start: 0.8145 (t) cc_final: 0.7734 (p) REVERT: R 230 PHE cc_start: 0.7250 (m-80) cc_final: 0.7004 (m-80) REVERT: R 233 ARG cc_start: 0.7270 (ttt180) cc_final: 0.7048 (ttt180) REVERT: R 240 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.4711 (tptp) REVERT: R 292 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6576 (tp) REVERT: R 441 MET cc_start: 0.5981 (mmt) cc_final: 0.5589 (mmt) REVERT: R 465 GLU cc_start: 0.5847 (tp30) cc_final: 0.5575 (tp30) outliers start: 25 outliers final: 19 residues processed: 144 average time/residue: 0.2335 time to fit residues: 45.3879 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 240 LYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 98 optimal weight: 0.0470 chunk 106 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 13 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.162402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130554 restraints weight = 11452.682| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.10 r_work: 0.3469 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8684 Z= 0.334 Angle : 0.568 6.577 11807 Z= 0.308 Chirality : 0.044 0.171 1352 Planarity : 0.004 0.042 1514 Dihedral : 4.423 17.233 1215 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.70 % Allowed : 17.54 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1113 helix: 1.16 (0.25), residues: 441 sheet: -0.34 (0.32), residues: 233 loop : -0.61 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 329 HIS 0.006 0.002 HIS A 347 PHE 0.028 0.002 PHE R 315 TYR 0.022 0.002 TYR R 191 ARG 0.004 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7013 (mptt) cc_final: 0.6691 (mmtt) REVERT: A 254 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7484 (t0) REVERT: A 258 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7466 (mp0) REVERT: B 32 GLN cc_start: 0.6955 (tt0) cc_final: 0.6690 (tp40) REVERT: B 68 ARG cc_start: 0.7367 (ttt180) cc_final: 0.6966 (ttt90) REVERT: B 220 GLN cc_start: 0.7357 (mt0) cc_final: 0.6993 (tt0) REVERT: B 322 ASP cc_start: 0.7500 (m-30) cc_final: 0.6834 (t0) REVERT: G 42 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7027 (mt-10) REVERT: N 77 ASN cc_start: 0.6591 (m-40) cc_final: 0.6371 (t0) REVERT: N 94 TYR cc_start: 0.8193 (m-80) cc_final: 0.7920 (m-80) REVERT: N 124 VAL cc_start: 0.8185 (t) cc_final: 0.7976 (p) REVERT: P 6 GLN cc_start: 0.5535 (tt0) cc_final: 0.5065 (mm-40) REVERT: R 240 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.4783 (tptp) REVERT: R 441 MET cc_start: 0.6092 (mmt) cc_final: 0.5366 (mmt) REVERT: R 465 GLU cc_start: 0.5930 (tp30) cc_final: 0.5685 (tp30) outliers start: 31 outliers final: 26 residues processed: 146 average time/residue: 0.2372 time to fit residues: 46.7660 Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 240 LYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 374 ASN Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.164467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132632 restraints weight = 11260.399| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.10 r_work: 0.3499 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8684 Z= 0.183 Angle : 0.476 5.530 11807 Z= 0.262 Chirality : 0.041 0.161 1352 Planarity : 0.003 0.039 1514 Dihedral : 4.087 16.143 1215 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.74 % Allowed : 18.50 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1113 helix: 1.44 (0.25), residues: 439 sheet: -0.28 (0.32), residues: 231 loop : -0.51 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.030 0.002 PHE R 315 TYR 0.018 0.001 TYR R 191 ARG 0.004 0.000 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7358 (m-30) cc_final: 0.6771 (m-30) REVERT: A 216 LYS cc_start: 0.6914 (mptt) cc_final: 0.6533 (mmtt) REVERT: A 258 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7396 (mp0) REVERT: B 68 ARG cc_start: 0.7413 (ttt180) cc_final: 0.7047 (ttt90) REVERT: B 220 GLN cc_start: 0.7307 (mt0) cc_final: 0.6948 (tt0) REVERT: B 264 TYR cc_start: 0.7432 (m-80) cc_final: 0.6994 (m-80) REVERT: B 322 ASP cc_start: 0.7439 (m-30) cc_final: 0.6759 (t0) REVERT: G 42 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7081 (mt-10) REVERT: G 58 GLU cc_start: 0.6826 (pm20) cc_final: 0.6487 (pm20) REVERT: G 62 ARG cc_start: 0.4990 (pmt-80) cc_final: 0.3785 (mmm160) REVERT: N 46 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6983 (mt-10) REVERT: N 94 TYR cc_start: 0.8095 (m-80) cc_final: 0.7681 (m-80) REVERT: R 231 MET cc_start: 0.7440 (mtp) cc_final: 0.6963 (mtp) REVERT: R 240 LYS cc_start: 0.5720 (OUTLIER) cc_final: 0.4632 (tptp) REVERT: R 441 MET cc_start: 0.6098 (mmt) cc_final: 0.5737 (mmt) REVERT: R 465 GLU cc_start: 0.5965 (tp30) cc_final: 0.5707 (tp30) outliers start: 23 outliers final: 20 residues processed: 140 average time/residue: 0.2720 time to fit residues: 52.7548 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 240 LYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 374 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.0170 chunk 24 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136001 restraints weight = 11097.991| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.14 r_work: 0.3517 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8684 Z= 0.126 Angle : 0.448 7.761 11807 Z= 0.244 Chirality : 0.039 0.155 1352 Planarity : 0.003 0.038 1514 Dihedral : 3.791 17.123 1215 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.91 % Allowed : 19.45 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1113 helix: 1.89 (0.26), residues: 431 sheet: 0.07 (0.33), residues: 228 loop : -0.38 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS P 9 PHE 0.031 0.001 PHE R 315 TYR 0.019 0.001 TYR R 191 ARG 0.003 0.000 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.6969 (mptt) cc_final: 0.6596 (mmtt) REVERT: A 258 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7432 (mp0) REVERT: B 16 ASN cc_start: 0.5527 (m110) cc_final: 0.4705 (m110) REVERT: B 20 ASP cc_start: 0.5968 (m-30) cc_final: 0.5676 (m-30) REVERT: B 55 LEU cc_start: 0.7319 (mt) cc_final: 0.7117 (mt) REVERT: B 68 ARG cc_start: 0.7492 (ttt180) cc_final: 0.7181 (ttt90) REVERT: B 217 MET cc_start: 0.7571 (mtt) cc_final: 0.7328 (mtm) REVERT: B 322 ASP cc_start: 0.7425 (m-30) cc_final: 0.6765 (t0) REVERT: G 42 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7196 (mt-10) REVERT: G 62 ARG cc_start: 0.4851 (pmt-80) cc_final: 0.3755 (mmm-85) REVERT: N 46 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7002 (mt-10) REVERT: N 74 ASN cc_start: 0.7820 (m-40) cc_final: 0.7464 (m-40) REVERT: N 77 ASN cc_start: 0.6004 (t0) cc_final: 0.5751 (t0) REVERT: N 94 TYR cc_start: 0.8063 (m-80) cc_final: 0.7414 (m-80) REVERT: R 231 MET cc_start: 0.7443 (mtp) cc_final: 0.6961 (mtp) REVERT: R 240 LYS cc_start: 0.5596 (OUTLIER) cc_final: 0.4545 (tptp) REVERT: R 292 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6802 (tp) REVERT: R 465 GLU cc_start: 0.6127 (tp30) cc_final: 0.5849 (tp30) outliers start: 16 outliers final: 14 residues processed: 150 average time/residue: 0.3095 time to fit residues: 64.0205 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 240 LYS Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.164094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132864 restraints weight = 11201.773| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.12 r_work: 0.3512 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8684 Z= 0.180 Angle : 0.470 6.069 11807 Z= 0.256 Chirality : 0.040 0.160 1352 Planarity : 0.003 0.041 1514 Dihedral : 3.902 15.579 1215 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.51 % Allowed : 19.69 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1113 helix: 1.73 (0.25), residues: 440 sheet: -0.04 (0.32), residues: 234 loop : -0.35 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS P 9 PHE 0.031 0.002 PHE N 68 TYR 0.019 0.001 TYR R 191 ARG 0.003 0.000 ARG N 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5770.22 seconds wall clock time: 102 minutes 57.72 seconds (6177.72 seconds total)